SEQUENCE AND STRUCTURE DEPENDENCE OF THE HYBRIDIZATION-TRIGGERED REACTION OF OLIGONUCLEOTIDES BEARING CONJUGATED CYCLOPROPAPYRROLOINDOLE

Oligodeoxyribonucleotides (ODNs) with conjugated reactive groups are p otential sequence-specific gene inactivating agents. The antitumor ant ibiotic CC-1065 binds preferably in the minor groove of A-T-rich sites of double-stranded DNA, and the cyclopropapyrroloindole (CPI) subunit of the drug alleviates adenines at their N3 position. Pure enantiomer ic (+)- and (-)-CPI and its N5-methyl homologue (MCPI) were synthesize d and conjugated to an ODN. These conjugates were evaluated for their ability to alkylate a target containing a duplex region immediately ad jacent to a single-stranded complementary binding region for the ODN c onjugate. The conjugates demonstrated excellent stability in physiolog ic conditions and stereospecific, hybridization-triggered alkylation o f the synthetic ODN targets. The dependence of the reaction rates on s equence of the duplex target region was in accord with the predicted m inor groove binding of the conjugated CPI. The reactivity was highly d ependent on the structure of the cross-linking group. Natural (+)-enan tiomers alkylate 10-20 times faster than the corresponding (-)-enantio mers. Regiospecificity of the alkylation reaction is conferred by the length of the spacer arm. N5-Methylation of the CPI moiety suppresses the reactivity by a factor of 3-5. Addition of a 1,2-dihydro-3H-pyrrol o[3,2-e]indole-7-carboxylate (DPI) binding subunit of CC-1065 between CPI or MCPI residues and an ODN results in a significant enhancement o f the reactivity which is especially pronounced for (-)-enantiomers, T he main products of sequence-specific alkylation were determined for c omplexes with the most efficient reactions.